Cd-hit manual

CD-HIT helps to significantly reduce the computational and manual efforts in many sequence analysis tasks and aids in understanding the data structure and correct the bias within a dataset. The CD-HIT package has CD-HIT, CD-HIT-2D, CD-HIT-EST, CD-HIT-EST-2D, CD-HIT, CD-HIT-PARA, PSI-CD-HIT, CD-HIT-OTU, CD-HIT-LAP, CD-HIT-DUP and over a dozen scripts. CD-HIT stands for Cluster Database at High Identity with Tolerance. The program (cd-hit) takes a fasta format sequence database as input and produces a set of . CD-HIT-2D compares 2 protein datasets (db1, db2). It identifies the sequences in db2 that are similar to db1 at a certain threshold. The input are two protein datasets (db1, db2) in fasta format and the output are two files: a fasta file of proteins in db2 that are not similar to db1 and a text file that lists similar sequences between db1 db2.

CD-HIT-2D compares 2 protein datasets (db1, db2). It identifies the sequences in db2 that are similar to db1 at a certain threshold. The input are two protein datasets (db1, db2) in fasta format and the output are two files: a fasta file of proteins in db2 that are not similar to db1 and a text file that lists similar sequences between db1 db2. cd-hit-est (www.doorway.ru) is a very widely used program for clustering and comparing large sets of DNA sequences. cd-hit-est is very fast and can handle extremely large databases. cd-hit helps to significantly reduce the computational and manual efforts in many sequence analysis tasks and aids in understanding the data structure and correct the bias within a dataset. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Weizhong Li Adam Godzik. Bioinformatics ()

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